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Jul 8

OntoKG: Ontology-Oriented Knowledge Graph Construction with Intrinsic-Relational Routing

Organizing a large-scale knowledge graph into a typed property graph requires structural decisions -- which entities become nodes, which properties become edges, and what schema governs these choices. Existing approaches embed these decisions in pipeline code or extract relations ad hoc, producing schemas that are tightly coupled to their construction process and difficult to reuse for downstream ontology-level tasks. We present an ontology-oriented approach in which the schema is designed from the outset for ontology analysis, entity disambiguation, domain customization, and LLM-guided extraction -- not merely as a byproduct of graph building. The core mechanism is intrinsic-relational routing, which classifies every property as either intrinsic or relational and routes it to the corresponding schema module. This routing produces a declarative schema that is portable across storage backends and independently reusable. We instantiate the approach on the January 2026 Wikidata dump. A rule-based cleaning stage identifies a 34.6M-entity core set from the full dump, followed by iterative intrinsic-relational routing that assigns each property to one of 94 modules organized into 8 categories. With tool-augmented LLM support and human review, the schema reaches 93.3% category coverage and 98.0% module assignment among classified entities. Exporting this schema yields a property graph with 34.0M nodes and 61.2M edges across 38 relationship types. We validate the ontology-oriented claim through five applications that consume the schema independently of the construction pipeline: ontology structure analysis, benchmark annotation auditing, entity disambiguation, domain customization, and LLM-guided extraction.

  • 4 authors
·
Apr 2

Valentine: Evaluating Matching Techniques for Dataset Discovery

Data scientists today search large data lakes to discover and integrate datasets. In order to bring together disparate data sources, dataset discovery methods rely on some form of schema matching: the process of establishing correspondences between datasets. Traditionally, schema matching has been used to find matching pairs of columns between a source and a target schema. However, the use of schema matching in dataset discovery methods differs from its original use. Nowadays schema matching serves as a building block for indicating and ranking inter-dataset relationships. Surprisingly, although a discovery method's success relies highly on the quality of the underlying matching algorithms, the latest discovery methods employ existing schema matching algorithms in an ad-hoc fashion due to the lack of openly-available datasets with ground truth, reference method implementations, and evaluation metrics. In this paper, we aim to rectify the problem of evaluating the effectiveness and efficiency of schema matching methods for the specific needs of dataset discovery. To this end, we propose Valentine, an extensible open-source experiment suite to execute and organize large-scale automated matching experiments on tabular data. Valentine includes implementations of seminal schema matching methods that we either implemented from scratch (due to absence of open source code) or imported from open repositories. The contributions of Valentine are: i) the definition of four schema matching scenarios as encountered in dataset discovery methods, ii) a principled dataset fabrication process tailored to the scope of dataset discovery methods and iii) the most comprehensive evaluation of schema matching techniques to date, offering insight on the strengths and weaknesses of existing techniques, that can serve as a guide for employing schema matching in future dataset discovery methods.

  • 9 authors
·
Oct 14, 2020

LinkAlign: Scalable Schema Linking for Real-World Large-Scale Multi-Database Text-to-SQL

Schema linking is a critical bottleneck in applying existing Text-to-SQL models to real-world, large-scale, multi-database environments. Through error analysis, we identify two major challenges in schema linking: (1) Database Retrieval: accurately selecting the target database from a large schema pool, while effectively filtering out irrelevant ones; and (2) Schema Item Grounding: precisely identifying the relevant tables and columns within complex and often redundant schemas for SQL generation. Based on these, we introduce LinkAlign, a novel framework tailored for large-scale databases with thousands of fields. LinkAlign comprises three key steps: multi-round semantic enhanced retrieval and irrelevant information isolation for Challenge 1, and schema extraction enhancement for Challenge 2. Each stage supports both Agent and Pipeline execution modes, enabling balancing efficiency and performance via modular design. To enable more realistic evaluation, we construct AmbiDB, a synthetic dataset designed to reflect the ambiguity of real-world schema linking. Experiments on widely-used Text-to-SQL benchmarks demonstrate that LinkAlign consistently outperforms existing baselines on all schema linking metrics. Notably, it improves the overall Text-to-SQL pipeline and achieves a new state-of-the-art score of 33.09% on the Spider 2.0-Lite benchmark using only open-source LLMs, ranking first on the leaderboard at the time of submission. The codes are available at https://github.com/Satissss/LinkAlign

  • 2 authors
·
Mar 24, 2025

APEX-SQL: Talking to the data via Agentic Exploration for Text-to-SQL

Text-to-SQL systems powered by Large Language Models have excelled on academic benchmarks but struggle in complex enterprise environments. The primary limitation lies in their reliance on static schema representations, which fails to resolve semantic ambiguity and scale effectively to large, complex databases. To address this, we propose APEX-SQL, an Agentic Text-to-SQL Framework that shifts the paradigm from passive translation to agentic exploration. Our framework employs a hypothesis-verification loop to ground model reasoning in real data. In the schema linking phase, we use logical planning to verbalize hypotheses, dual-pathway pruning to reduce the search space, and parallel data profiling to validate column roles against real data, followed by global synthesis to ensure topological connectivity. For SQL generation, we introduce a deterministic mechanism to retrieve exploration directives, allowing the agent to effectively explore data distributions, refine hypotheses, and generate semantically accurate SQLs. Experiments on BIRD (70.65% execution accuracy) and Spider 2.0-Snow (51.01% execution accuracy) demonstrate that APEX-SQL outperforms competitive baselines with reduced token consumption. Further analysis reveals that agentic exploration acts as a performance multiplier, unlocking the latent reasoning potential of foundation models in enterprise settings. Ablation studies confirm the critical contributions of each component in ensuring robust and accurate data analysis.

  • 6 authors
·
Feb 11

Matchmaker: Self-Improving Large Language Model Programs for Schema Matching

Schema matching -- the task of finding matches between attributes across disparate data sources with different tables and hierarchies -- is critical for creating interoperable machine learning (ML)-ready data. Addressing this fundamental data-centric problem has wide implications, especially in domains like healthcare, finance and e-commerce -- but also has the potential to benefit ML models more generally, by increasing the data available for ML model training. However, schema matching is a challenging ML task due to structural/hierarchical and semantic heterogeneity between different schemas. Previous ML approaches to automate schema matching have either required significant labeled data for model training, which is often unrealistic or suffer from poor zero-shot performance. To this end, we propose Matchmaker - a compositional language model program for schema matching, comprised of candidate generation, refinement and confidence scoring. Matchmaker also self-improves in a zero-shot manner without the need for labeled demonstrations via a novel optimization approach, which constructs synthetic in-context demonstrations to guide the language model's reasoning process. Empirically, we demonstrate on real-world medical schema matching benchmarks that Matchmaker outperforms previous ML-based approaches, highlighting its potential to accelerate data integration and interoperability of ML-ready data.

  • 2 authors
·
Oct 31, 2024

Youtu-GraphRAG: Vertically Unified Agents for Graph Retrieval-Augmented Complex Reasoning

Graph retrieval-augmented generation (GraphRAG) has effectively enhanced large language models in complex reasoning by organizing fragmented knowledge into explicitly structured graphs. Prior efforts have been made to improve either graph construction or graph retrieval in isolation, yielding suboptimal performance, especially when domain shifts occur. In this paper, we propose a vertically unified agentic paradigm, Youtu-GraphRAG, to jointly connect the entire framework as an intricate integration. Specifically, (i) a seed graph schema is introduced to bound the automatic extraction agent with targeted entity types, relations and attribute types, also continuously expanded for scalability over unseen domains; (ii) To obtain higher-level knowledge upon the schema, we develop novel dually-perceived community detection, fusing structural topology with subgraph semantics for comprehensive knowledge organization. This naturally yields a hierarchical knowledge tree that supports both top-down filtering and bottom-up reasoning with community summaries; (iii) An agentic retriever is designed to interpret the same graph schema to transform complex queries into tractable and parallel sub-queries. It iteratively performs reflection for more advanced reasoning; (iv) To alleviate the knowledge leaking problem in pre-trained LLM, we propose a tailored anonymous dataset and a novel 'Anonymity Reversion' task that deeply measures the real performance of the GraphRAG frameworks. Extensive experiments across six challenging benchmarks demonstrate the robustness of Youtu-GraphRAG, remarkably moving the Pareto frontier with up to 90.71% saving of token costs and 16.62% higher accuracy over state-of-the-art baselines. The results indicate our adaptability, allowing seamless domain transfer with minimal intervention on schema.

tencent Tencent
·
Aug 27, 2025 1

Parallelizing Linear Transformers with the Delta Rule over Sequence Length

Transformers with linear attention (i.e., linear transformers) and state-space models have recently been suggested as a viable linear-time alternative to transformers with softmax attention. However, these models still underperform transformers especially on tasks that require in-context retrieval. While more expressive variants of linear transformers which replace the additive outer-product update in linear transformers with the delta rule have been found to be more effective at associative recall, existing algorithms for training such models do not parallelize over sequence length and are thus inefficient to train on modern hardware. This work describes a hardware-efficient algorithm for training linear transformers with the delta rule, which exploits a memory-efficient representation for computing products of Householder matrices. This algorithm allows us to scale up DeltaNet to standard language modeling settings. We train a 1.3B model for 100B tokens and find that it outperforms recent linear-time baselines such as Mamba and GLA in terms of perplexity and zero-shot performance on downstream tasks (including on tasks that focus on recall). We also experiment with two hybrid models which combine DeltaNet layers with (1) sliding-window attention layers every other layer or (2) two global attention layers, and find that these hybrid models outperform strong transformer baselines.

  • 5 authors
·
Jun 10, 2024 2

DFIN-SQL: Integrating Focused Schema with DIN-SQL for Superior Accuracy in Large-Scale Databases

The task of converting natural language queries into SQL queries is intricate, necessitating a blend of precise techniques for an accurate translation. The DIN-SQL (Decomposed-In-Context SQL) methodology represents a significant development in this domain. This paper introduces DFIN (Decomposed Focused-In-Context), an innovative extension of DIN-SQL that enhances Text-to-SQL conversion by addressing schema linking errors, which are a major source of inaccuracies. DFIN uniquely alternates between prompting techniques and Retrieval-Augmented Generation (RAG), adapting to the size and complexity of the database schema. A preprocessing phase embeds database definitions and leverages annotated files, akin to those in the BIRD dataset, facilitating the runtime retrieval of pertinent schema information. This strategy significantly reduces the token count for schema linking prompts, enabling the use of a standard GPT-4 model over its larger context variant, thus handling large-scale databases more effectively and economically. Our evaluation on the BIRD dataset, a challenging real-world benchmark, demonstrates that DFIN not only scales efficiently but also improves accuracy, achieving a score of 51.69. This improvement surpasses DIN-SQL method (the current third-place), which is the highest-ranked model employing in-context learning rather than fine-tuning, previously scoring 50.72. The advancement of DFIN underscores the evolving capabilities of in-context learning methodologies combined with advanced language models, offering a promising avenue for future research in complex Text-to-SQL conversion tasks.

  • 3 authors
·
Mar 1, 2024

DELTA: Dynamic Layer-Aware Token Attention for Efficient Long-Context Reasoning

Large reasoning models (LRMs) achieve state-of-the-art performance on challenging benchmarks by generating long chains of intermediate steps, but their inference cost is dominated by decoding, where each new token must attend to the entire growing sequence. Existing sparse attention methods reduce computation by pruning the key-value (KV) cache, yet they suffer from severe accuracy degradation on reasoning tasks due to cumulative selection errors and the dynamic importance of tokens over long derivations. We present DELTA, a training-free sparse attention mechanism that achieves computational efficiency without sacrificing model accuracy. DELTA partitions transformer layers into three groups: initial layers that use full attention, a small set of selection layers that identify salient tokens via aggregated head-level attention scores, and subsequent sparse-attention layers that attend only to the selected subset. This design preserves the full KV cache in GPU memory for accuracy, while avoiding expensive full-attention computation over many layers. On reasoning benchmarks such as AIME and GPQA-Diamond, DELTA matches or surpasses full attention in accuracy, while reducing the number of attended tokens by up to 5times and delivering 1.5times end-to-end speedup. Our results show that selective reuse of intermediate attention maps offers a robust path toward efficient long-context reasoning.

  • 4 authors
·
Oct 10, 2025

XiYan-SQL: A Multi-Generator Ensemble Framework for Text-to-SQL

To tackle the challenges of large language model performance in natural language to SQL tasks, we introduce XiYan-SQL, an innovative framework that employs a multi-generator ensemble strategy to improve candidate generation. We introduce M-Schema, a semi-structured schema representation method designed to enhance the understanding of database structures. To enhance the quality and diversity of generated candidate SQL queries, XiYan-SQL integrates the significant potential of in-context learning (ICL) with the precise control of supervised fine-tuning. On one hand, we propose a series of training strategies to fine-tune models to generate high-quality candidates with diverse preferences. On the other hand, we implement the ICL approach with an example selection method based on named entity recognition to prevent overemphasis on entities. The refiner optimizes each candidate by correcting logical or syntactical errors. To address the challenge of identifying the best candidate, we fine-tune a selection model to distinguish nuances of candidate SQL queries. The experimental results on multiple dialect datasets demonstrate the robustness of XiYan-SQL in addressing challenges across different scenarios. Overall, our proposed XiYan-SQL achieves the state-of-the-art execution accuracy of 89.65% on the Spider test set, 69.86% on SQL-Eval, 41.20% on NL2GQL, and a competitive score of 72.23% on the Bird development benchmark. The proposed framework not only enhances the quality and diversity of SQL queries but also outperforms previous methods.

  • 13 authors
·
Nov 13, 2024

DeltaProduct: Improving State-Tracking in Linear RNNs via Householder Products

Linear Recurrent Neural Networks (linear RNNs) have emerged as competitive alternatives to Transformers for sequence modeling, offering efficient training and linear-time inference. However, existing architectures face a fundamental trade-off between expressivity and efficiency, dictated by the structure of their state-transition matrices. Diagonal matrices, used in models such as Mamba, GLA, or mLSTM, yield fast runtime but have limited expressivity. To address this, recent architectures such as DeltaNet and RWKV-7 adopted a diagonal plus rank-1 structure, which allows simultaneous token and channel mixing, improving associative recall and, as recently shown, state-tracking when allowing negative eigenvalues in the state-transition matrices. Building on the interpretation of DeltaNet's recurrence as performing one step of online gradient descent per token on an associative recall loss, we introduce DeltaProduct, which instead takes multiple (n_h) steps per token. This naturally leads to diagonal plus rank-n_h state-transition matrices, formed as products of n_h generalized Householder transformations, providing a tunable mechanism to balance expressivity and efficiency. We provide a detailed theoretical characterization of the state-tracking capability of DeltaProduct in finite precision, showing how it improves by increasing n_h. Our extensive experiments demonstrate that DeltaProduct outperforms DeltaNet in both state-tracking and language modeling, while also showing significantly improved length extrapolation capabilities.

  • 6 authors
·
Feb 14, 2025

Knowledge Graph-based Retrieval-Augmented Generation for Schema Matching

Traditional similarity-based schema matching methods are incapable of resolving semantic ambiguities and conflicts in domain-specific complex mapping scenarios due to missing commonsense and domain-specific knowledge. The hallucination problem of large language models (LLMs) also makes it challenging for LLM-based schema matching to address the above issues. Therefore, we propose a Knowledge Graph-based Retrieval-Augmented Generation model for Schema Matching, referred to as the KG-RAG4SM. In particular, KG-RAG4SM introduces novel vector-based, graph traversal-based, and query-based graph retrievals, as well as a hybrid approach and ranking schemes that identify the most relevant subgraphs from external large knowledge graphs (KGs). We showcase that KG-based retrieval-augmented LLMs are capable of generating more accurate results for complex matching cases without any re-training. Our experimental results show that KG-RAG4SM outperforms the LLM-based state-of-the-art (SOTA) methods (e.g., Jellyfish-8B) by 35.89% and 30.50% in terms of precision and F1 score on the MIMIC dataset, respectively; KG-RAG4SM with GPT-4o-mini outperforms the pre-trained language model (PLM)-based SOTA methods (e.g., SMAT) by 69.20% and 21.97% in terms of precision and F1 score on the Synthea dataset, respectively. The results also demonstrate that our approach is more efficient in end-to-end schema matching, and scales to retrieve from large KGs. Our case studies on the dataset from the real-world schema matching scenario exhibit that the hallucination problem of LLMs for schema matching is well mitigated by our solution.

  • 4 authors
·
Jan 15, 2025

What's In Your Field? Mapping Scientific Research with Knowledge Graphs and Large Language Models

The scientific literature's exponential growth makes it increasingly challenging to navigate and synthesize knowledge across disciplines. Large language models (LLMs) are powerful tools for understanding scientific text, but they fail to capture detailed relationships across large bodies of work. Unstructured approaches, like retrieval augmented generation, can sift through such corpora to recall relevant facts; however, when millions of facts influence the answer, unstructured approaches become cost prohibitive. Structured representations offer a natural complement -- enabling systematic analysis across the whole corpus. Recent work enhances LLMs with unstructured or semistructured representations of scientific concepts; to complement this, we try extracting structured representations using LLMs. By combining LLMs' semantic understanding with a schema of scientific concepts, we prototype a system that answers precise questions about the literature as a whole. Our schema applies across scientific fields and we extract concepts from it using only 20 manually annotated abstracts. To demonstrate the system, we extract concepts from 30,000 papers on arXiv spanning astrophysics, fluid dynamics, and evolutionary biology. The resulting database highlights emerging trends and, by visualizing the knowledge graph, offers new ways to explore the ever-growing landscape of scientific knowledge. Demo: abby101/surveyor-0 on HF Spaces. Code: https://github.com/chiral-carbon/kg-for-science.

  • 4 authors
·
Mar 12, 2025

Probabilistic Reasoning via Deep Learning: Neural Association Models

In this paper, we propose a new deep learning approach, called neural association model (NAM), for probabilistic reasoning in artificial intelligence. We propose to use neural networks to model association between any two events in a domain. Neural networks take one event as input and compute a conditional probability of the other event to model how likely these two events are to be associated. The actual meaning of the conditional probabilities varies between applications and depends on how the models are trained. In this work, as two case studies, we have investigated two NAM structures, namely deep neural networks (DNN) and relation-modulated neural nets (RMNN), on several probabilistic reasoning tasks in AI, including recognizing textual entailment, triple classification in multi-relational knowledge bases and commonsense reasoning. Experimental results on several popular datasets derived from WordNet, FreeBase and ConceptNet have all demonstrated that both DNNs and RMNNs perform equally well and they can significantly outperform the conventional methods available for these reasoning tasks. Moreover, compared with DNNs, RMNNs are superior in knowledge transfer, where a pre-trained model can be quickly extended to an unseen relation after observing only a few training samples. To further prove the effectiveness of the proposed models, in this work, we have applied NAMs to solving challenging Winograd Schema (WS) problems. Experiments conducted on a set of WS problems prove that the proposed models have the potential for commonsense reasoning.

  • 7 authors
·
Mar 24, 2016

Schema for In-Context Learning

In-Context Learning (ICL) enables transformer-based language models to adapt to new tasks by conditioning on demonstration examples. However, traditional example-driven in-context learning lacks explicit modules for knowledge retrieval and transfer at the abstraction level. Inspired by cognitive science, specifically schema theory, which holds that humans interpret new information by activating pre-existing mental frameworks (schemas) to structure understanding, we introduce SCHEMA ACTIVATED IN CONTEXT LEARNING (SA-ICL). This framework extracts the representation of the building blocks of cognition for the reasoning process instilled from prior examples, creating an abstracted schema, a lightweight, structured template of key inferential steps and their relationships, which is then used to augment a model's reasoning process when presented with a novel question. We demonstrate that a broad range of large language models (LLMs) lack the capacity to form and utilize internal schema-based learning representations implicitly, but instead benefit significantly from explicit schema-based scaffolding. Across chemistry and physics questions from the GPQA dataset, our experiments show that SA-ICL consistently boosts performance, up to 36.19 percent, when the single demonstration example is of high quality, which simultaneously reduces reliance on the number of demonstrations and enhances interpretability. SCHEMA ACTIVATED IN CONTEXT LEARNING not only bridges disparate ICL strategies ranging from pattern priming to Chain-of-Thought prompting, but also paves a new path for enhancing human-like reasoning in LLMs.

  • 7 authors
·
Oct 14, 2025

Kaczmarz Linear Attention

Long-context language modeling remains central to modern sequence modeling, but the quadratic cost of Transformer attention makes scaling computationally prohibitive. Linear recurrent models address this bottleneck by compressing the context into a fixed-size state, making the rule that forgets, writes, and edits information a central design problem. To address state maintenance, Gated DeltaNet (GDN) combines gated state decay with delta-rule residual writes, using a learnable coefficient to balance forgetting and update magnitude. However, this coefficient is learned empirically rather than derived from the underlying objective, which can lead to suboptimal update magnitudes. We revisit the online-regression objective underlying GDN and, inspired by the Kaczmarz projection method, derive the key-norm-normalized dynamic step size β_t = η_t / (|k_t|_2^2 + ε) for residual updates. We propose Kaczmarz Linear Attention (KLA), a one-scalar modification of GDN that preserves the state shape, gates, linear recurrence, and chunkwise parallel algorithm. At the 0.4B scale with a 1B-token budget, KLA achieves the lowest validation perplexity among evaluated linear-time baselines, 8.09 versus 8.50 for GDN, and remains stable up to 65K tokens. On controlled tasks, KLA reaches 100% on single-needle-in-a-haystack retrieval, improves 8x multi-query associative recall by 7.03 points over GDN, and delivers 2.1x higher decode throughput at 32K context. These results suggest that the key-norm-normalized Kaczmarz coefficient is a first-order design axis for delta-rule sequence models: it improves accuracy, extrapolation, and decoding efficiency without changing the recurrent state or hardware kernel.

  • 3 authors
·
May 8

What Makes a Maze Look Like a Maze?

A unique aspect of human visual understanding is the ability to flexibly interpret abstract concepts: acquiring lifted rules explaining what they symbolize, grounding them across familiar and unfamiliar contexts, and making predictions or reasoning about them. While off-the-shelf vision-language models excel at making literal interpretations of images (e.g., recognizing object categories such as tree branches), they still struggle to make sense of such visual abstractions (e.g., how an arrangement of tree branches may form the walls of a maze). To address this challenge, we introduce Deep Schema Grounding (DSG), a framework that leverages explicit structured representations of visual abstractions for grounding and reasoning. At the core of DSG are schemas--dependency graph descriptions of abstract concepts that decompose them into more primitive-level symbols. DSG uses large language models to extract schemas, then hierarchically grounds concrete to abstract components of the schema onto images with vision-language models. The grounded schema is used to augment visual abstraction understanding. We systematically evaluate DSG and different methods in reasoning on our new Visual Abstractions Dataset, which consists of diverse, real-world images of abstract concepts and corresponding question-answer pairs labeled by humans. We show that DSG significantly improves the abstract visual reasoning performance of vision-language models, and is a step toward human-aligned understanding of visual abstractions.

  • 5 authors
·
Sep 12, 2024

BIRDNet: Mining and Encoding Boolean Implication Knowledge Graphs as Interpretable Deep Neural Networks

Tabular data in knowledge-rich domains often carries a latent prior in the form of Boolean implication relationships (BIRs) between pairs of features. We mine such relationships with a sparse-exception binomial test. The mined implications form a typed directed graph, equivalent to a propositional rule base of 2-literal clauses. We encode this graph as the connectivity of a layered neural network, called BIRDNet, in which each hidden unit corresponds to one mined rule and binds only to its two features. We show two consequences of this design: First, the architecture is sparse by construction: at most 2/d of the weights in each BIR layer are active, where d is the input dimension. Second, the model is interpretable: every trained unit keeps a stable symbolic identity, so rules can be read off the network without surrogate models. Unlike most neurosymbolic models, BIRDNet does not consume an external rule base; its structural prior is mined from the data. We evaluate BIRDNet on six transcriptomic and proteomic benchmarks. Our results show that BIRDNet stays within 0.02 AUROC of the strongest dense baseline, at a small accuracy cost, while using up to 96times fewer active parameters than an architecture-matched dense MLP. First-layer rules recover known biological signatures across multiple cancer subtypes and tissue types, including canonical amplicons, lineage-defining co-expression modules, and immune-infiltration markers. Data and code are available at: https://github.com/MAHI-Group/BIRDNet.

  • 1 authors
·
May 27

Solving Formal Math Problems by Decomposition and Iterative Reflection

General-purpose Large Language Models (LLMs) have achieved remarkable success in intelligence, performing comparably to human experts on complex reasoning tasks such as coding and mathematical reasoning. However, generating formal proofs in specialized languages like Lean 4 remains a significant challenge for these models, limiting their application in complex theorem proving and automated verification. Current approaches typically require specializing models through fine-tuning on dedicated formal corpora, incurring high costs for data collection and training. In this work, we introduce Delta Prover, an agent-based framework that orchestrates the interaction between a general-purpose LLM and the Lean 4 proof environment. Delta Prover leverages the reflection and reasoning capabilities of general-purpose LLMs to interactively construct formal proofs in Lean 4, circumventing the need for model specialization. At its core, the agent integrates two novel, interdependent components: an algorithmic framework for reflective decomposition and iterative proof repair, and a custom Domain-Specific Language (DSL) built upon Lean 4 for streamlined subproblem management. Delta Prover achieves a state-of-the-art 95.9\% success rate on the miniF2F-test benchmark, surpassing all existing approaches, including those requiring model specialization. Furthermore, Delta Prover exhibits a significantly stronger test-time scaling law compared to standard Best-of-N proof strategies. Crucially, our findings demonstrate that general-purpose LLMs, when guided by an effective agentic structure, possess substantial untapped theorem-proving capabilities. This presents a computationally efficient alternative to specialized models for robust automated reasoning in formal environments.

  • 17 authors
·
Jul 20, 2025

MAG-SQL: Multi-Agent Generative Approach with Soft Schema Linking and Iterative Sub-SQL Refinement for Text-to-SQL

Recent In-Context Learning based methods have achieved remarkable success in Text-to-SQL task. However, there is still a large gap between the performance of these models and human performance on datasets with complex database schema and difficult questions, such as BIRD. Besides, existing work has neglected to supervise intermediate steps when solving questions iteratively with question decomposition methods, and the schema linking methods used in these works are very rudimentary. To address these issues, we propose MAG-SQL, a multi-agent generative approach with soft schema linking and iterative Sub-SQL refinement. In our framework, an entity-based method with tables' summary is used to select the columns in database, and a novel targets-conditions decomposition method is introduced to decompose those complex questions. Additionally, we build a iterative generating module which includes a Sub-SQL Generator and Sub-SQL Refiner, introducing external oversight for each step of generation. Through a series of ablation studies, the effectiveness of each agent in our framework has been demonstrated. When evaluated on the BIRD benchmark with GPT-4, MAG-SQL achieves an execution accuracy of 61.08\%, compared to the baseline accuracy of 46.35\% for vanilla GPT-4 and the baseline accuracy of 57.56\% for MAC-SQL. Besides, our approach makes similar progress on Spider.

  • 3 authors
·
Aug 15, 2024

PIPE-Cypher: Automatic Enterprise Benchmark Generation for Text-to-Cypher Systems

Enterprise property graphs vary widely in schema structure, internal terminology, domain assumptions, governance constraints, and user interaction patterns. A deployment-relevant Text2Cypher benchmark therefore reflects the questions users and agents actually ask of that graph. Creating such a benchmark is difficult because schemas and values are unique, and graph structure changes over time. Each NL-query pair must also be executable, use real graph entities, preserve diversity, and remain balanced across query types and difficulty levels. We present PIPE-Cypher, a local benchmark-generation pipeline that turns a live property graph and optional seed queries from customer questions, analyst logs, or agent tool calls into balanced NL-to-Cypher benchmarks. PIPE-Cypher combines schema profiling, reverse-query grounding, constrained generation, deterministic Cypher governance, execution validation, redaction, diversity controls, and a calibrated local LLM judge. Using local Qwen3.5-9B generation and judging, PIPE-Cypher exports 3,000 accepted FinBench/SNB examples, completes three audited ablation suites, calibrates judge behavior with human labels, and evaluates 11 local downstream models. The resulting benchmark is deliberately discriminative: zero-shot transfer is weak, while a few-shot control shows that schema-specific example banks can help compatible model families. Together, PIPE-Cypher makes Text2Cypher benchmarking a repeatable process that evolves with the graph, its users, and its target workloads.

Higher-Order Knowledge Representations for Agentic Scientific Reasoning

Scientific inquiry requires systems-level reasoning that integrates heterogeneous experimental data, cross-domain knowledge, and mechanistic evidence into coherent explanations. While Large Language Models (LLMs) offer inferential capabilities, they often depend on retrieval-augmented contexts that lack structural depth. Traditional Knowledge Graphs (KGs) attempt to bridge this gap, yet their pairwise constraints fail to capture the irreducible higher-order interactions that govern emergent physical behavior. To address this, we introduce a methodology for constructing hypergraph-based knowledge representations that faithfully encode multi-entity relationships. Applied to a corpus of ~1,100 manuscripts on biocomposite scaffolds, our framework constructs a global hypergraph of 161,172 nodes and 320,201 hyperedges, revealing a scale-free topology (power law exponent ~1.23) organized around highly connected conceptual hubs. This representation prevents the combinatorial explosion typical of pairwise expansions and explicitly preserves the co-occurrence context of scientific formulations. We further demonstrate that equipping agentic systems with hypergraph traversal tools, specifically using node-intersection constraints, enables them to bridge semantically distant concepts. By exploiting these higher-order pathways, the system successfully generates grounded mechanistic hypotheses for novel composite materials, such as linking cerium oxide to PCL scaffolds via chitosan intermediates. This work establishes a "teacherless" agentic reasoning system where hypergraph topology acts as a verifiable guardrail, accelerating scientific discovery by uncovering relationships obscured by traditional graph methods.

  • 2 authors
·
Jan 8

A Frame is Worth One Token: Efficient Generative World Modeling with Delta Tokens

Anticipating diverse future states is a central challenge in video world modeling. Discriminative world models produce a deterministic prediction that implicitly averages over possible futures, while existing generative world models remain computationally expensive. Recent work demonstrates that predicting the future in the feature space of a vision foundation model (VFM), rather than a latent space optimized for pixel reconstruction, requires significantly fewer world model parameters. However, most such approaches remain discriminative. In this work, we introduce DeltaTok, a tokenizer that encodes the VFM feature difference between consecutive frames into a single continuous "delta" token, and DeltaWorld, a generative world model operating on these tokens to efficiently generate diverse plausible futures. Delta tokens reduce video from a three-dimensional spatio-temporal representation to a one-dimensional temporal sequence, for example yielding a 1,024x token reduction with 512x512 frames. This compact representation enables tractable multi-hypothesis training, where many futures are generated in parallel and only the best is supervised. At inference, this leads to diverse predictions in a single forward pass. Experiments on dense forecasting tasks demonstrate that DeltaWorld forecasts futures that more closely align with real-world outcomes, while having over 35x fewer parameters and using 2,000x fewer FLOPs than existing generative world models. Code and weights: https://deltatok.github.io.

amazon Amazon
·
Apr 5 2

KnowCoder: Coding Structured Knowledge into LLMs for Universal Information Extraction

In this paper, we propose KnowCoder, a Large Language Model (LLM) to conduct Universal Information Extraction (UIE) via code generation. KnowCoder aims to develop a kind of unified schema representation that LLMs can easily understand and an effective learning framework that encourages LLMs to follow schemas and extract structured knowledge accurately. To achieve these, KnowCoder introduces a code-style schema representation method to uniformly transform different schemas into Python classes, with which complex schema information, such as constraints among tasks in UIE, can be captured in an LLM-friendly manner. We further construct a code-style schema library covering over 30,000 types of knowledge, which is the largest one for UIE, to the best of our knowledge. To ease the learning process of LLMs, KnowCoder contains a two-phase learning framework that enhances its schema understanding ability via code pretraining and its schema following ability via instruction tuning. After code pretraining on around 1.5B automatically constructed data, KnowCoder already attains remarkable generalization ability and achieves relative improvements by 49.8% F1, compared to LLaMA2, under the few-shot setting. After instruction tuning, KnowCoder further exhibits strong generalization ability on unseen schemas and achieves up to 12.5% and 21.9%, compared to sota baselines, under the zero-shot setting and the low resource setting, respectively. Additionally, based on our unified schema representations, various human-annotated datasets can simultaneously be utilized to refine KnowCoder, which achieves significant improvements up to 7.5% under the supervised setting.

  • 17 authors
·
Mar 12, 2024

DeltaLLM: A Training-Free Framework Exploiting Temporal Sparsity for Efficient Edge LLM Inference

Deploying Large Language Models (LLMs) on edge devices remains challenging due to their quadratically increasing computations with the sequence length. Existing studies for dynamic attention pruning are designed for hardware with massively parallel computation capabilities, such as GPUs or TPUs, and aim at long context lengths (e.g., 64K), making them unsuitable for edge scenarios. We present DeltaLLM, a training-free framework that exploits temporal sparsity in attention patterns to enable efficient LLM inference across both the prefilling and decoding stages, on resource-constrained edge devices. DeltaLLM introduces an accuracy- and memory-aware delta matrix construction strategy that introduces temporal sparsity, and a context-aware hybrid attention mechanism that combines full attention in a local context window with delta approximation outside it to increase accuracy. We evaluate our framework on the edge-device-friendly BitNet-b1.58-2B-4T model and Llama3.2-1B-Instruct model across diverse language tasks. The results show that on BitNet, our framework increases the attention sparsity from 0% to 60% during the prefilling stage with slight accuracy improvement on the WG task, and 0% to 57% across both the prefilling and decoding stages, with even higher F1 score from 29.63 to 30.97 on SQuAD-v2 task. On the Llama model, it can also achieve up to 60% sparsity during the prefilling stage and around 57% across both stages with negligible accuracy drop. These results demonstrate that DeltaLLM offers a promising solution for efficient edge deployment, requiring no fine-tuning and seamlessly integrating with existing inference pipelines.

  • 4 authors
·
Jul 25, 2025

DocSage: An Information Structuring Agent for Multi-Doc Multi-Entity Question Answering

Multi-document Multi-entity Question Answering inherently demands models to track implicit logic between multiple entities across scattered documents. However, existing Large Language Models (LLMs) and Retrieval-Augmented Generation (RAG) frameworks suffer from critical limitations: standard RAG's vector similarity-based coarse-grained retrieval often omits critical facts, graph-based RAG fails to efficiently integrate fragmented complex relationship networks, and both lack schema awareness, leading to inadequate cross-document evidence chain construction and inaccurate entity relationship deduction. To address these challenges, we propose DocSage, an end-to-end agentic framework that integrates dynamic schema discovery, structured information extraction, and schema-aware relational reasoning with error guarantees. DocSage operates through three core modules: (1) A schema discovery module dynamically infers query-specific minimal joinable schemas to capture essential entities and relationships; (2) An extraction module transforms unstructured text into semantically coherent relational tables, enhanced by error-aware correction mechanisms to reduce extraction errors; (3) A reasoning module performs multi-hop relational reasoning over structured tables, leveraging schema awareness to efficiently align cross-document entities and aggregate evidence. This agentic design offers three key advantages: precise fact localization via SQL-powered indexing, natural support for cross-document entity joins through relational tables, and mitigated LLM attention diffusion via structured representation. Evaluations on two MDMEQA benchmarks demonstrate that DocSage significantly outperforms state-of-the-art long-context LLMs and RAG systems, achieving more than 27% accuracy improvements respectively.

  • 5 authors
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Mar 11

Gated DeltaNet-2: Decoupling Erase and Write in Linear Attention

Linear attention replaces the unbounded cache of softmax attention with a fixed-size recurrent state, reducing sequence mixing to linear time and decoding to constant memory. The hard part is not just what to forget, but how to edit this compressed memory without scrambling existing associations. Delta-rule models subtract the current read before writing a new value, and Kimi Delta Attention (KDA) sharpens forgetting with channel-wise decay. But the active edit still uses a single scalar gate to control two different things: how much old content to erase on the key side and how much new content to commit on the value side. We introduce Gated DeltaNet-2, which generalizes both Gated DeltaNet and KDA by inheriting adaptive forgetting and channel-wise decay while addressing their shared limitation, the scalar tie between erasing and writing. Gated Delta Rule-2 separates these roles with a channel-wise erase gate b_t and a channel-wise write gate w_t, reducing to KDA when both gates collapse to the same scalar and to Gated DeltaNet when the decay also collapses. We derive a fast-weight update view, a chunkwise WY algorithm with channel-wise decay absorbed into asymmetric erase factors, and a gate-aware backward pass that preserves efficient parallel training. At 1.3B parameters trained on 100B FineWeb-Edu tokens, Gated DeltaNet-2 achieves the strongest overall results among Mamba-2, Gated DeltaNet, KDA, and Mamba-3 variants across language modeling, commonsense reasoning, and retrieval. Its advantage is most pronounced on long-context RULER needle-in-a-haystack benchmarks, where it improves the evaluated multi-key retrieval setting and remains strong in both recurrent and hybrid settings. Code is available at https://github.com/NVlabs/GatedDeltaNet-2.

nvidia NVIDIA
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May 20 1

meta4: semantically-aligned generation of metaphoric gestures using self-supervised text and speech representation

Image Schemas are repetitive cognitive patterns that influence the way we conceptualize and reason about various concepts present in speech. These patterns are deeply embedded within our cognitive processes and are reflected in our bodily expressions including gestures. Particularly, metaphoric gestures possess essential characteristics and semantic meanings that align with Image Schemas, to visually represent abstract concepts. The shape and form of gestures can convey abstract concepts, such as extending the forearm and hand or tracing a line with hand movements to visually represent the image schema of PATH. Previous behavior generation models have primarily focused on utilizing speech (acoustic features and text) to drive the generation model of virtual agents. They have not considered key semantic information as those carried by Image Schemas to effectively generate metaphoric gestures. To address this limitation, we introduce META4, a deep learning approach that generates metaphoric gestures from both speech and Image Schemas. Our approach has two primary goals: computing Image Schemas from input text to capture the underlying semantic and metaphorical meaning, and generating metaphoric gestures driven by speech and the computed image schemas. Our approach is the first method for generating speech driven metaphoric gestures while leveraging the potential of Image Schemas. We demonstrate the effectiveness of our approach and highlight the importance of both speech and image schemas in modeling metaphoric gestures.

  • 3 authors
·
Nov 9, 2023

Fast and Stable Triangular Inversion for Delta-Rule Linear Transformers

Linear attention has emerged as a cornerstone for efficient long-context architectures, as evidenced by its integration into state-of-the-art open-source models including Qwen3.5/3.6, Kimi Linear, and RWKV-7. Models that incorporate linear attention layers with the so-called Delta-Rule involve the inversion of triangular matrices as a core sub-routine. This operation often forms a performance bottleneck, and, due to its high-sensitivity to numerical errors, it can significantly deteriorate end-to-end model accuracy if it is not carefully implemented. This work provides a systematic analysis of both direct and iterative triangular inversion algorithms, targeting methods that are rich in matrix products, and, therefore, have the potential to efficiently utilize modern hardware. To that end, our analysis covers a broad spectrum of mathematical and practical aspects, with a heavy focus on numerical stability, computational complexity, and, ultimately, hardware efficiency and practical considerations. We provide a rigorous experimental evaluation to verify these properties in practical scenarios, and in low-precision floating-point representations, highlighting the strengths and limitations of each method. Performance benchmarks on NPUs reveal up to 4.3times speed-up against the state-of-the-art implementations of SGLang for triangular matrix inversion, leading to significant performance improvements on the entire layer level, while maintaining full end-to-end model accuracy.

  • 7 authors
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May 19

Graph schemas as abstractions for transfer learning, inference, and planning

Transferring latent structure from one environment or problem to another is a mechanism by which humans and animals generalize with very little data. Inspired by cognitive and neurobiological insights, we propose graph schemas as a mechanism of abstraction for transfer learning. Graph schemas start with latent graph learning where perceptually aliased observations are disambiguated in the latent space using contextual information. Latent graph learning is also emerging as a new computational model of the hippocampus to explain map learning and transitive inference. Our insight is that a latent graph can be treated as a flexible template -- a schema -- that models concepts and behaviors, with slots that bind groups of latent nodes to the specific observations or groundings. By treating learned latent graphs (schemas) as prior knowledge, new environments can be quickly learned as compositions of schemas and their newly learned bindings. We evaluate graph schemas on two previously published challenging tasks: the memory & planning game and one-shot StreetLearn, which are designed to test rapid task solving in novel environments. Graph schemas can be learned in far fewer episodes than previous baselines, and can model and plan in a few steps in novel variations of these tasks. We also demonstrate learning, matching, and reusing graph schemas in more challenging 2D and 3D environments with extensive perceptual aliasing and size variations, and show how different schemas can be composed to model larger and more complex environments. To summarize, our main contribution is a unified system, inspired and grounded in cognitive science, that facilitates rapid transfer learning of new environments using schemas via map-induction and composition that handles perceptual aliasing.

  • 9 authors
·
Feb 14, 2023

Structured Context Engineering for File-Native Agentic Systems: Evaluating Schema Accuracy, Format Effectiveness, and Multi-File Navigation at Scale

Large Language Model agents increasingly operate external systems through programmatic interfaces, yet practitioners lack empirical guidance on how to structure the context these agents consume. Using SQL generation as a proxy for programmatic agent operations, we present a systematic study of context engineering for structured data, comprising 9,649 experiments across 11 models, 4 formats (YAML, Markdown, JSON, Token-Oriented Object Notation [TOON]), and schemas ranging from 10 to 10,000 tables. Our findings challenge common assumptions. First, architecture choice is model-dependent: file-based context retrieval improves accuracy for frontier-tier models (Claude, GPT, Gemini; +2.7%, p=0.029) but shows mixed results for open source models (aggregate -7.7%, p<0.001), with deficits varying substantially by model. Second, format does not significantly affect aggregate accuracy (chi-squared=2.45, p=0.484), though individual models, particularly open source, exhibit format-specific sensitivities. Third, model capability is the dominant factor, with a 21 percentage point accuracy gap between frontier and open source tiers that dwarfs any format or architecture effect. Fourth, file-native agents scale to 10,000 tables through domain-partitioned schemas while maintaining high navigation accuracy. Fifth, file size does not predict runtime efficiency: compact or novel formats can incur a token overhead driven by grep output density and pattern unfamiliarity, with the magnitude depending on model capability. These findings provide practitioners with evidence-based guidance for deploying LLM agents on structured systems, demonstrating that architectural decisions should be tailored to model capability rather than assuming universal best practices.

  • 1 authors
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Feb 5

HyDRA: A Hybrid-Driven Reasoning Architecture for Verifiable Knowledge Graphs

The synergy between symbolic knowledge, often represented by Knowledge Graphs (KGs), and the generative capabilities of neural networks is central to advancing neurosymbolic AI. A primary bottleneck in realizing this potential is the difficulty of automating KG construction, which faces challenges related to output reliability, consistency, and verifiability. These issues can manifest as structural inconsistencies within the generated graphs, such as the formation of disconnected isolated islands of data or the inaccurate conflation of abstract classes with specific instances. To address these challenges, we propose HyDRA, a Hybrid-Driven Reasoning Architecture designed for verifiable KG automation. Given a domain or an initial set of documents, HyDRA first constructs an ontology via a panel of collaborative neurosymbolic agents. These agents collaboratively agree on a set of competency questions (CQs) that define the scope and requirements the ontology must be able to answer. Given these CQs, we build an ontology graph that subsequently guides the automated extraction of triplets for KG generation from arbitrary documents. Inspired by design-by-contracts (DbC) principles, our method leverages verifiable contracts as the primary control mechanism to steer the generative process of Large Language Models (LLMs). To verify the output of our approach, we extend beyond standard benchmarks and propose an evaluation framework that assesses the functional correctness of the resulting KG by leveraging symbolic verifications as described by the neurosymbolic AI framework, SymbolicAI. This work contributes a hybrid-driven architecture for improving the reliability of automated KG construction and the exploration of evaluation methods for measuring the functional integrity of its output. The code is publicly available.

  • 5 authors
·
Jul 21, 2025

OSDN: Improving Delta Rule with Provable Online Preconditioning in Linear Attention

Linear attention and state-space models offer constant-memory alternatives to softmax attention, but often struggle with in-context associative recall. The Delta Rule mitigates this by writing each token via one step of online gradient descent. However, its step size relies on a single scalar gate that ignores the feature-wise curvature of the inner objective. We propose Online Scaled DeltaNet (OSDN), which augments the scalar gate with a diagonal preconditioner updated online via hypergradient feedback. Crucially, this right-preconditioning is algebraically equivalent to a per-feature scaling of the write-side key. This equivalence allows OSDN to strictly preserve the hardware-friendly chunkwise parallel pipeline of DeltaNet without incurring high-dimensional state overhead. Theoretically, by exploiting the exact-quadratic structure of the inner regression loss, we establish super-geometric convergence against a right-Newton comparator and prove an algorithm-aligned token-local residual contraction bound. To handle non-stationary contexts, we further introduce Adaptive Preconditioner Forgetting (APF) to dynamically refresh stale calibration. Empirically, OSDN demonstrates strong performance across scales. At the 340M-parameter scale, OSDN improves JRT-style in-context recall by 32% over DeltaNet. Scaling to 1.3B parameters, it achieves a 39% reduction in the recall residual ratio while maintaining parity on general downstream tasks (e.g., perplexity and LongBench) -- demonstrating that our online-preconditioning mechanism effectively transfers and amplifies at the billion-parameter scale.

  • 6 authors
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May 12

The Delta Learning Hypothesis: Preference Tuning on Weak Data can Yield Strong Gains

Improvements in language models are often driven by improving the quality of the data we train them on, which can be limiting when strong supervision is scarce. In this work, we show that paired preference data consisting of individually weak data points can enable gains beyond the strength of each individual data point. We formulate the delta learning hypothesis to explain this phenomenon, positing that the relative quality delta between points suffices to drive learning via preference tuning--even when supervised finetuning on the weak data hurts. We validate our hypothesis in controlled experiments and at scale, where we post-train 8B models on preference data generated by pairing a small 3B model's responses with outputs from an even smaller 1.5B model to create a meaningful delta. Strikingly, on a standard 11-benchmark evaluation suite (MATH, MMLU, etc.), our simple recipe matches the performance of Tulu 3, a state-of-the-art open model tuned from the same base model while relying on much stronger supervisors (e.g., GPT-4o). Thus, delta learning enables simpler and cheaper open recipes for state-of-the-art post-training. To better understand delta learning, we prove in logistic regression that the performance gap between two weak teacher models provides useful signal for improving a stronger student. Overall, our work shows that models can learn surprisingly well from paired data that might typically be considered weak.

  • 7 authors
·
Jul 8, 2025

Diversed Model Discovery via Structured Table Discovery

Model cards describe model behavior through a mixture of textual descriptions and structured artifacts, including performance, configuration, and dataset tables. Existing model search systems rely predominantly on semantic similarity over text, which can produce homogeneous result sets and limit exploration of alternatives. We argue that model search is inherently comparative: users want models that are task-aligned yet differentiated in measurable ways. We hypothesize that this balance requires retrieval over condensed, high-quality evidence rather than verbose descriptions, and much of that evidence is concentrated in structured tables. We present StructuredSemanticSearch, a table-driven model search framework built on the ModelTables benchmark. Given a query, StructuredSemanticSearch combines a semantic baseline for task alignment with a structure-aware pipeline that discovers query-related model-card tables using table discovery operators such as unionability, joinability, and keyword search. Retrieved tables are mapped back to model cards under a controlled top-k budget, enabling fair comparison between text-based and table-based retrieval. Beyond retrieval, StructuredSemanticSearch adapts table integration to the model-table domain through orientation-aware integration, producing compact integrated views of tables from partially overlapping and sometimes transposed evidence tables. For evaluation, we introduce a nugget-based, auditable protocol that extracts compact evidence items from model cards, matches queries to condition- or intent-specific nuggets, and measures evidence coverage and diversity over retrieved model-card candidate sets. This protocol also provides a scalable path toward approximate, evidence-based labeling in dynamic model lakes. Experiments on 597 model-recommendation queries show improved nugget coverage for the structure-aware pipeline than semantic baseline

Periodical embeddings uncover hidden interdisciplinary patterns in the subject classification scheme of science

Subject classification schemes are foundational to the organization, evaluation, and navigation of scientific knowledge. While expert-curated systems like Scopus provide widely used taxonomies, they often suffer from coarse granularity, subjectivity, and limited adaptability to emerging interdisciplinary fields. Data-driven alternatives based on citation networks show promise but lack rigorous, external validation against the semantic content of scientific literature. Here, we propose a novel quantitative framework that leverages classification tasks to evaluate the effectiveness of journal classification schemes. Using over 23 million paper abstracts, we demonstrate that labels derived from k-means clustering on Periodical2Vec (P2V)--a periodical embedding learned from paper-level citations--yield significantly higher classification performance than both Scopus and other data-driven baselines (e.g., citation, co-citation, and Node2Vec variants). By comparing journal partitions across classification schemes, two structural patterns emerge on the map of science: (1) the reorganization of disciplinary boundaries--splitting overly broad categories (e.g., "Medicine" into "Oncology", "Cardiology", and other specialties) while merging artificially fragmented ones (e.g., "Chemistry" and "Chemical Engineering"); and (2) the identification of coherent interdisciplinary clusters--such as "Biomedical Engineering", "Medical Ethics", and "Information Management"--that are dispersed across multiple categories but unified in citation space. These findings underscore that citation-derived periodical embeddings not only outperform traditional taxonomies in predictive validity but also offer a dynamic, fine-grained map of science that better reflects both the specialization and interdisciplinarity inherent in contemporary research.

  • 2 authors
·
Dec 27, 2025

AceMap: Knowledge Discovery through Academic Graph

The exponential growth of scientific literature requires effective management and extraction of valuable insights. While existing scientific search engines excel at delivering search results based on relational databases, they often neglect the analysis of collaborations between scientific entities and the evolution of ideas, as well as the in-depth analysis of content within scientific publications. The representation of heterogeneous graphs and the effective measurement, analysis, and mining of such graphs pose significant challenges. To address these challenges, we present AceMap, an academic system designed for knowledge discovery through academic graph. We present advanced database construction techniques to build the comprehensive AceMap database with large-scale academic entities that contain rich visual, textual, and numerical information. AceMap also employs innovative visualization, quantification, and analysis methods to explore associations and logical relationships among academic entities. AceMap introduces large-scale academic network visualization techniques centered on nebular graphs, providing a comprehensive view of academic networks from multiple perspectives. In addition, AceMap proposes a unified metric based on structural entropy to quantitatively measure the knowledge content of different academic entities. Moreover, AceMap provides advanced analysis capabilities, including tracing the evolution of academic ideas through citation relationships and concept co-occurrence, and generating concise summaries informed by this evolutionary process. In addition, AceMap uses machine reading methods to generate potential new ideas at the intersection of different fields. Exploring the integration of large language models and knowledge graphs is a promising direction for future research in idea evolution. Please visit https://www.acemap.info for further exploration.

  • 26 authors
·
Mar 4, 2024

Semantic Level of Detail for Knowledge Graphs: Discovering Abstraction Boundaries via Spectral Heat Diffusion

Graph-structured knowledge systems -- from knowledge graphs to GraphRAG pipelines -- organize information into hierarchical communities, yet lack a principled mechanism for continuous resolution control: where do the qualitative boundaries between abstraction levels lie, and how should an agent navigate them? Current approaches rely on discrete community detection with manually tuned resolution parameters (e.g., Leiden γ), offering no continuous zoom and no formal guarantees. We introduce Semantic Level of Detail (SLoD), a framework that addresses both problems by defining a continuous zoom operator via heat kernel diffusion on a graph Laplacian whose kNN structure is induced by a Poincare-ball embedding. We prove hierarchical coherence in the tree limit (exact tree with Sarkar embedding), with bounded approximation error, and demonstrate consistent boundary-detection behaviour on noisy hierarchies; spectral gaps in the graph Laplacian then induce emergent scale boundaries -- scales where the representation undergoes qualitative transitions -- detectable without manual resolution tuning. On synthetic hierarchies (HSBM, 1024 nodes), spectral clustering at the BoundaryScan-detected scale recovers planted levels, with macro ARI saturating at 1.00 in the high-SNR regime (50-seed median) and meso ARI reaching 0.89 [0.86, 0.92] at r=200. On the full WordNet noun hierarchy (82K synsets), using 100 stratified leaf queries, detected boundaries align with true taxonomic depth (τ= 0.79), demonstrating meaningful abstraction-level discovery in real-world knowledge graphs without resolution-parameter tuning. The composite weights, MAD threshold, and kNN-parameter rule (k = max(10, min(lfloorNrfloor, 50))) use defaults that transferred unchanged between HSBM and WordNet; their behaviour on graphs with implicit or qualitatively different hierarchical structure is open.

  • 1 authors
·
Apr 30

DisasterLex: An Expert Concept-to-Schema Knowledge Graph for Geospatial Reasoning in Disaster Analytics

Disasters are inevitable and increasingly costly, and effective response depends on querying structured tabular data: precise, information-dense records of hazard, exposure, vulnerability, and lifeline infrastructure that underpin disaster management. Current text-to-SQL methods enable natural-language access to such tables but transfer poorly to the disaster domain, where queries span heterogeneous geospatial schemas and require reasoning over causal relations. We introduce DisasterLex, a knowledge-graph-mediated framework that inserts an Expert Knowledge Graph (EKG) of curated concepts and typed causal edges between the user query and the database, bridged to schema by concept-to-table links. The orchestration runs four stages (identifying query entities, routing to the operational domain, planning over causal edges, and grounding the SQL), restricting the schema passed to the model at each step. We instantiate it on a disaster-analytics database (36 geospatial tables, 150 columns) with an EKG of 107 concepts, 117 causal edges, and 52 concept-to-schema links, evaluated on a 75-query test set. On all seven base models spanning proprietary and open-weight families, DisasterLex beats four state-of-the-art baselines (LightRAG, HippoRAG 2, ReFoRCE, CHESS) by 1.4x to 2.75x, with absolute scores of 1.65 to 3.56 (of 5.0). Error analysis shows baseline failures cluster in routing and multi-table SQL composition, the operations our orchestration explicitly addresses. Code, data, and the EKG artifact are available at https://github.com/YimingXiao98/DisasterLex and on Zenodo at https://doi.org/10.5281/zenodo.20388029.

  • 6 authors
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May 27

Agents-K1: Towards Agent-native Knowledge Orchestration

Current LLM-based research agents have advanced through agent orchestration, yet largely overlook scientific knowledge orchestration. Existing works often reduce papers to abstracts, surface mentions, and flat cites edges, omitting key entities, claims, evidence, mechanisms, and method lineages essential for scientific reasoning. To this end, we introduce Agents-K1, an end-to-end knowledge orchestration pipeline that converts raw documents into agent-native scientific knowledge graphs. Agents-K1 integrates three components under a unifying theoretical foundation: a multimodal parser whose five-module schema captures entities, multimodal evidence, citations, and typed inter-entity relations across the full paper rather than abstracts alone; a 4B information-extraction backbone trained with GRPO under a rule-based reward; and a graphanything CLI, a tri-source agent interface that unifies web search, multimodal graph retrieval, and cross-document traversal. On top of this, we process 2.46 million scientific papers across six subjects to produce Scholar-KG, of which we release a one-million-paper subset, and the full Scholar-KG is accessible via the SCP link below. The same pipeline can be extended to general-domain corpora and to schema-conformant data synthesis. Extensive experiments demonstrate that Agents-K1 achieves superior performance in scientific information extraction, knowledge graph construction, and multi-hop scientific reasoning.

  • 25 authors
·
Jun 10

CodeS: Towards Building Open-source Language Models for Text-to-SQL

Language models have shown promising performance on the task of translating natural language questions into SQL queries (Text-to-SQL). However, most of the state-of-the-art (SOTA) approaches rely on powerful yet closed-source large language models (LLMs), such as ChatGPT and GPT-4, which may have the limitations of unclear model architectures, data privacy risks, and expensive inference overheads. To address the limitations, we introduce CodeS, a series of pre-trained language models with parameters ranging from 1B to 15B, specifically designed for the text-to-SQL task. CodeS is a fully open-source language model, which achieves superior accuracy with much smaller parameter sizes. This paper studies the research challenges in building CodeS. To enhance the SQL generation abilities of CodeS, we adopt an incremental pre-training approach using a specifically curated SQL-centric corpus. Based on this, we address the challenges of schema linking and rapid domain adaptation through strategic prompt construction and a bi-directional data augmentation technique. We conduct comprehensive evaluations on multiple datasets, including the widely used Spider benchmark, the newly released BIRD benchmark, robustness-diagnostic benchmarks such as Spider-DK, Spider-Syn, Spider-Realistic, and Dr.Spider, as well as two real-world datasets created for financial and academic applications. The experimental results show that our CodeS achieves new SOTA accuracy and robustness on nearly all challenging text-to-SQL benchmarks.

  • 10 authors
·
Feb 26, 2024

Delta Attention Residuals

Attention Residuals replace standard additive residual connections with learned softmax attention over previous layer outputs, enabling selective cross-layer routing. However, standard Attention Residuals still attend over cumulative hidden states in previous layers, which are highly redundant. We show that this redundancy leads to routing collapse in deeper layers: attention weights become low-contrast and closer to uniform (max weight {approx}0.2), limiting the model's ability to select informative states in previous layers. This raises a key but underexplored design question: what layer-wise representations should be routed in Attention Residuals? To answer this question, we propose Delta Attention Residuals, which attend over deltas -- the change introduced by each sublayer (v_i = h_{i+1} - h_i) -- instead of cumulative states. Delta representations are structurally diverse and yield higher-contrast attention distributions (max weight {approx}0.6), enabling more selective and effective routing across layers. This principle applies at both per-sublayer and block granularity. Across all tested scales (220M--7.6B), Delta Attention Residuals consistently outperform both standard residuals and Attention Residuals, with 1.7--8.2\% validation perplexity gains. Delta Attention Residuals also enables converting pretrained checkpoints into Delta Attention Residuals via standard fine-tuning. Code is available at https://github.com/wdlctc/delta-attention-residuals-code.

  • 3 authors
·
May 12 4

OptimusKG: Unifying biomedical knowledge in a modern multimodal graph

Biomedical knowledge graphs (KGs) are widely used in the life sciences, yet many are derived from unstructured documents and therefore lack schema-level constrains, whereas graphs assembled from structured resources are difficult to harmonize into a unified representation. We present OptimusKG, a multimodal biomedical labeled property graph (LPG) built from structured and semi-structured resources to preserve factual, type-specific metadata across molecular, anatomical, clinical, and environmental domains. OptimusKG contains 190,531 nodes across 10 entity types, 21,813,816 edges across 26 relation types, and 67,249,863 property instances encoding 110,276,843 values across 150 distinct property keys, derived from 18 ontologies and controlled vocabularies. The graph enforces a top-level schema for nodes and edges and retains granular, type-specific properties, cross-references, and provenance across molecular, anatomical, clinical, and environmental domains. We assessed the validity of OptimusKG by evaluating whether graph relationships are supported by evidence from the scientific literature using a multimodal agent, PaperQA3. PaperQA3 identified supporting evidence for 70.0% of sampled edges, whereas 83.4% of sampled false edges received no supporting evidence. Edges without literature support were concentrated in associations derived from experimental and functional genomics resources, suggesting that OptimusKG captures biomedical knowledge that may precede synthesis in the scientific literature. OptimusKG is distributed as Apache Parquet files, providing a standardized resource for graph-based machine learning, knowledge-grounded retrieval with large language models, and biomedical discovery use cases such as hypothesis generation.

  • 8 authors
·
Apr 28

Agentic Deep Graph Reasoning Yields Self-Organizing Knowledge Networks

We present an agentic, autonomous graph expansion framework that iteratively structures and refines knowledge in situ. Unlike conventional knowledge graph construction methods relying on static extraction or single-pass learning, our approach couples a reasoning-native large language model with a continually updated graph representation. At each step, the system actively generates new concepts and relationships, merges them into a global graph, and formulates subsequent prompts based on its evolving structure. Through this feedback-driven loop, the model organizes information into a scale-free network characterized by hub formation, stable modularity, and bridging nodes that link disparate knowledge clusters. Over hundreds of iterations, new nodes and edges continue to appear without saturating, while centrality measures and shortest path distributions evolve to yield increasingly distributed connectivity. Our analysis reveals emergent patterns, such as the rise of highly connected 'hub' concepts and the shifting influence of 'bridge' nodes, indicating that agentic, self-reinforcing graph construction can yield open-ended, coherent knowledge structures. Applied to materials design problems, we present compositional reasoning experiments by extracting node-specific and synergy-level principles to foster genuinely novel knowledge synthesis, yielding cross-domain ideas that transcend rote summarization and strengthen the framework's potential for open-ended scientific discovery. We discuss other applications in scientific discovery and outline future directions for enhancing scalability and interpretability.

  • 1 authors
·
Feb 18, 2025

DocCGen: Document-based Controlled Code Generation

Recent developments show that Large Language Models (LLMs) produce state-of-the-art performance on natural language (NL) to code generation for resource-rich general-purpose languages like C++, Java, and Python. However, their practical usage for structured domain-specific languages (DSLs) such as YAML, JSON is limited due to domain-specific schema, grammar, and customizations generally unseen by LLMs during pre-training. Efforts have been made to mitigate this challenge via in-context learning through relevant examples or by fine-tuning. However, it suffers from problems, such as limited DSL samples and prompt sensitivity but enterprises maintain good documentation of the DSLs. Therefore, we propose DocCGen, a framework that can leverage such rich knowledge by breaking the NL-to-Code generation task for structured code languages into a two-step process. First, it detects the correct libraries using the library documentation that best matches the NL query. Then, it utilizes schema rules extracted from the documentation of these libraries to constrain the decoding. We evaluate our framework for two complex structured languages, Ansible YAML and Bash command, consisting of two settings: Out-of-domain (OOD) and In-domain (ID). Our extensive experiments show that DocCGen consistently improves different-sized language models across all six evaluation metrics, reducing syntactic and semantic errors in structured code. We plan to open-source the datasets and code to motivate research in constrained code generation.

  • 6 authors
·
Jun 17, 2024

Workflow is All You Need: Escaping the "Statistical Smoothing Trap" via High-Entropy Information Foraging and Adversarial Pacing

Central to long-form text generation in vertical domains is the "impossible trinity" confronting current large language models (LLMs): the simultaneous achievement of low hallucination, deep logical coherence, and personalized expression. This study establishes that this bottleneck arises from existing generative paradigms succumbing to the Statistical Smoothing Trap, a phenomenon that overlooks the high-entropy information acquisition and structured cognitive processes integral to expert-level writing. To address this limitation, we propose the DeepNews Framework, an agentic workflow that explicitly models the implicit cognitive processes of seasoned financial journalists. The framework integrates three core modules: first, a dual-granularity retrieval mechanism grounded in information foraging theory, which enforces a 10:1 saturated information input ratio to mitigate hallucinatory outputs; second, schema-guided strategic planning, a process leveraging domain expert knowledge bases (narrative schemas) and Atomic Blocks to forge a robust logical skeleton; third, adversarial constraint prompting, a technique deploying tactics including Rhythm Break and Logic Fog to disrupt the probabilistic smoothness inherent in model-generated text. Experiments delineate a salient Knowledge Cliff in deep financial reporting: content truthfulness collapses when retrieved context falls below 15,000 characters, while a high-redundancy input exceeding 30,000 characters stabilizes the Hallucination-Free Rate (HFR) above 85%. In an ecological validity blind test conducted with a top-tier Chinese technology media outlet, the DeepNews system--built on a previous-generation model (DeepSeek-V3-0324)-achieved a 25% submission acceptance rate, significantly outperforming the 0% acceptance rate of zero-shot generation by a state-of-the-art (SOTA) model (GPT-5).

  • 1 authors
·
Dec 10, 2025

Leveraging Large Language Models for Generating Research Topic Ontologies: A Multi-Disciplinary Study

Ontologies and taxonomies of research fields are critical for managing and organising scientific knowledge, as they facilitate efficient classification, dissemination and retrieval of information. However, the creation and maintenance of such ontologies are expensive and time-consuming tasks, usually requiring the coordinated effort of multiple domain experts. Consequently, ontologies in this space often exhibit uneven coverage across different disciplines, limited inter-domain connectivity, and infrequent updating cycles. In this study, we investigate the capability of several large language models to identify semantic relationships among research topics within three academic domains: biomedicine, physics, and engineering. The models were evaluated under three distinct conditions: zero-shot prompting, chain-of-thought prompting, and fine-tuning on existing ontologies. Additionally, we assessed the cross-domain transferability of fine-tuned models by measuring their performance when trained in one domain and subsequently applied to a different one. To support this analysis, we introduce PEM-Rel-8K, a novel dataset consisting of over 8,000 relationships extracted from the most widely adopted taxonomies in the three disciplines considered in this study: MeSH, PhySH, and IEEE. Our experiments demonstrate that fine-tuning LLMs on PEM-Rel-8K yields excellent performance across all disciplines.

  • 4 authors
·
Aug 28, 2025